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Fast and accurate long-read alignment with Burrows-Wheeler transform.

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Scenic: single-cell regulatory network inference and clustering.

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Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer

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QPCTL regulates macrophage and monocyte abundance and inflammatory signatures in the tumor microenvironment

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Novel insights into HBV‐hepatocellular carcinoma at single‐cell sequencing

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Blockade of V‐domain immunoglobulin suppressor of T‐cell activation reprograms tumour‐associated macrophages and improves efficacy of PD‐1 inhibitor in gastric cancer

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cDC2 plasticity and acquisition of a DC3‐like phenotype mediated by IL‐6 and PGE2 in a patient‐derived colorectal cancer organoids model

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Defining and targeting macrophage heterogeneity in the mammary gland and breast cancer

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Development and Clinical Applications of Therapeutic Cancer Vaccines with Individualized and Shared Neoantigens

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FOLR2+ macrophages in cancer: allies or enemies

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Integrating computational pathology and multi-transcriptomics to characterize lung adenocarcinoma heterogeneity and prognostic modeling

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Single-cell RNA sequencing analysis revealed the immunosuppressive remodeling of tumor-associated macrophages mediated by the MIF-CD74 axis in gastric cancer

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Pan-cancer spatial atlas of tertiary lymphoid structures

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Niclosamide targets the dynamic progression of macrophages for the resolution of endometriosis in a mouse model

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circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment

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Single-Cell RNA Sequencing Reveals Heterogeneity in the Tumor Microenvironment between Young-Onset and Old-Onset Colorectal Cancer

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Heterogeneity of tumor-infiltrating myeloid cells in era of single-cell genomics

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Leveraging immune resistance archetypes in solid cancer to inform next-generation anticancer therapies

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The mycosis fungoides cutaneous microenvironment shapes dysfunctional cell trafficking, antitumor immunity, matrix interactions, and angiogenesis

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Novel T cell exhaustion gene signature to predict prognosis and immunotherapy response in thyroid carcinoma from integrated RNA-sequencing analysis

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TNFR1 signaling promotes pancreatic tumor growth by limiting dendritic cell number and function

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Comparative profiling of single-cell transcriptome reveals heterogeneity of tumor microenvironment between solid and acinar lung adenocarcinoma

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ChemR23 activation reprograms macrophages toward a less inflammatory phenotype and dampens carcinoma progression

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Tissue-resident macrophages — early passengers or drivers in the tumor niche?

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Subverted macrophages in the triple-negative breast cancer ecosystem

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A single-cell atlas of lung homeostasis reveals dynamic changes during development and aging

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IL-17A/CEBPβ/OPN/LYVE-1 axis inhibits anti-tumor immunity by promoting tumor-associated tissue-resident macrophages

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Immunotherapy biomarkers: the long and winding road

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Meta-Analysis of Single-Cell RNA-Seq Data Reveals the Mechanism of Formation and Heterogeneity of Tertiary Lymphoid Organ in Vascular Disease

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Insights into the heterogeneity of the tumor microenvironment in lung adenocarcinoma and squamous carcinoma through single‐cell transcriptomic analysis: Implications for distinct immunotherapy outcomes

Fang, X., Li, D., Wan, S., Hu, J., Zhang, P., Jie, D., Chen, L., Jiang, G., & Song, N. (2024) · The Journal of Gene Medicine · doi:10.1002/jgm.3694 · Cited by 20

Identification of SPP1+ macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics

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Single-cell RNA sequencing and spatial transcriptomics of esophageal squamous cell carcinoma with lymph node metastases

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Epithelial cell diversity and immune remodeling in bladder cancer progression: insights from single-cell transcriptomics

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Tebentafusp, a T cell engager, promotes macrophage reprogramming and in combination with IL-2 overcomes macrophage immunosuppression in cancer

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Astragalus polysaccharides inhibits tumor proliferation and enhances cisplatin sensitivity in bladder cancer by regulating the PI3K/AKT/FoxO1 axis

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Mast cells boost anti-tumor potency of MAIT cells via inflammasome-dependent secretion of IL-18

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Prognostic and immunological characteristics of CDK1 in lung adenocarcinoma: A systematic analysis

Du, Q., Liu, W., Mei, T., Wang, J., Qin, T., & Huang, D. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1128443 · Cited by 21

Single-Cell Profiling Reveals Sustained Immune Infiltration, Surveillance, and Tumor Heterogeneity in Infiltrative Basal Cell Carcinoma

Huang, L., Wang, X., Pei, S., Li, X., Dong, L., Bian, X., Sun, H., Jin, L., Hou, H., Shi, W., et al. (2023) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2023.04.020 · Cited by 20

Frenemies in the Microenvironment: Harnessing Mast Cells for Cancer Immunotherapy

Sulsenti, R., & Jachetti, E. (2023) · Pharmaceutics · doi:10.3390/pharmaceutics15061692 · Cited by 19

Extracellular vesicles derived from nasopharyngeal carcinoma induce the emergence of mature regulatory dendritic cells using a galectin‐9 dependent mechanism

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A pre-trained large generative model for translating single-cell transcriptomes to proteomes

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Combinations of Toll-like receptor 8 agonist TL8-506 activate human tumor-derived dendritic cells

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The dual role of CXCL9/SPP1 polarized tumor-associated macrophages in modulating anti-tumor immunity in hepatocellular carcinoma

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Sialylated CD43 forms a glyco-immune barrier that restrains antileukemic immunity

Chung, J., Vallurupalli, M., Noel, S., Schor, G., Mrowka, S., Scapozza, I., Demere, Z., Kammula, S. V., Hu, M., Kim, S. Y., et al. (2026) · Science · doi:10.1126/science.ady5196 · Cited by 18

Lysosomal acid lipase, CSF1R, and PD-L1 determine functions of CD11c+ myeloid-derived suppressor cells

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New hormone receptor-positive breast cancer mouse cell line mimicking the immune microenvironment of anti-PD-1 resistant mammary carcinoma

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Glycolysis regulation in tumor‐associated macrophages: Its role in tumor development and cancer treatment

Jiang, G., Hong, J., Sun, L., Wei, H., Gong, W., Wang, S., & Zhu, J. (2023) · International Journal of Cancer · doi:10.1002/ijc.34711 · Cited by 18

Immune Cells in the Tumor Microenvironment of Soft Tissue Sarcomas

Jumaniyazova, E. D., Lokhonina, А. V., Dzhalilova, D. S., Kosyreva, A. M., & Fatkhudinov, T. (2023) · Cancers · doi:10.3390/cancers15245760 · Cited by 20

Myeloid-T cell interplay and cell state transitions associated with checkpoint inhibitor response in melanoma

Schlenker, R., Schwalie, P. C., Dettling, S., Huesser, T., Irmisch, A., Mariani, M., Gómez, J. M. M., Ribeiro, A., Limani, F., Herter, S., et al. (2024) · Med · doi:10.1016/j.medj.2024.03.015 · Cited by 19

Breast Cancer Immune Landscape: Interplay Between Systemic and Local Immunity

Gerashchenko, T. S., Frolova, A. A., Patysheva, M. R., Fedorov, A. A., Stakheyeva, M. N., Denisov, E. V., & Чердынцева, Н. В. (2024) · Advanced Biology · doi:10.1002/adbi.202400140 · Cited by 21

Pediatric glioma immune profiling identifies TIM3 as a therapeutic target in BRAF fusion pilocytic astrocytoma

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Noninvasive in vivo imaging of macrophages: understanding tumor microenvironments and delivery of therapeutics

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Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma

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Fallopian tube single cell analysis reveals myeloid cell alterations in high-grade serous ovarian cancer

Brand, J., Haro, M., Lin, X., Rimel, B. J., McGregor, S. M., Lawrenson, K., & Dinh, H. Q. (2024) · iScience · doi:10.1016/j.isci.2024.108990 · Cited by 19

Single-cell sequencing reveals distinct immune cell features in cutaneous lesions of pemphigus vulgaris and bullous pemphigoid

Hu, Z. Q., Zheng, M., Guo, Z., Zhou, W., Zhou, W., Nan, Y., Zhang, G., Lu, Q., & Zhao, M. (2024) · Clinical Immunology · doi:10.1016/j.clim.2024.110219 · Cited by 17

Spatial Dynamics of T- and B-Cell Responses Predicts Clinical Outcome of Resectable and Unresectable Hepatocellular Carcinoma

Kurebayashi, Y., Sugimoto, K., Tsujikawa, H., Matsuda, K., Nomura, R., Ueno, A., Masugi, Y., Yamazaki, K., Effendi, K., Takeuchi, H., et al. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-24-0479 · Cited by 18

PLXDC1 + Tumor‐Associated Pancreatic Stellate Cells Promote Desmoplastic and Immunosuppressive Niche in Pancreatic Ductal Adenocarcinoma

Du, Y., Zhao, Y., Li, J., Wang, J., You, S., Zhang, Y., Zhang, L., Yang, J., Alinejad‐Rokny, H., Cheng, S., et al. (2025) · Advanced Science · doi:10.1002/advs.202415756 · Cited by 18

Multi-omics dissection of tumor microenvironment-mediated drug resistance: mechanisms and therapeutic reprogramming

Chen, F., Fu, Y., Bai, G., Qiu, J., & Hua, K. (2025) · Frontiers in Pharmacology · doi:10.3389/fphar.2025.1634413 · Cited by 19

Pan-Cancer Analyses Refine the Single-Cell Portrait of Tumor-Infiltrating Dendritic Cells

Ma, T., Chu, X., Wang, J., Li, X., Zhang, Y., Tong, D., Xu, W., Dang, G., Qi, L., Miao, Y., et al. (2025) · Cancer Research · doi:10.1158/0008-5472.can-24-3595 · Cited by 20

Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming

Lischetti, U., Liang, C.-Y., Carrara, M., Coelho, R., Hanns, A., Lombardo, F. C., Dondi, A., Goetze, S., Hensler, M., Kurzeder, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67557-z · Cited by 19

Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Yiu, S. P. T., Chang, Y., Yeo, Y. Y., Qiu, H., Wu, W., Michel, H. A., Jin, X., Huang, R., Kure, S., Parmelee, L. K., et al. (2026) · Cancer Discovery · doi:10.1158/2159-8290.cd-25-0775 · Cited by 17

Enabling CAR-T cells for solid tumors: Rage against the suppressive tumor microenvironment

Antoñana-Vildosola, A., Zanetti, S. R., & Palazón, A. (2022) · International review of cytology · doi:10.1016/bs.ircmb.2022.03.004 · Cited by 17

Combination IFNβ and Membrane-Stable CD40L Maximize Tumor Dendritic Cell Activation and Lymph Node Trafficking to Elicit Systemic T-cell Immunity

Zheng, H., Yu, X., Ibrahim, M. L., Foresman, D., Xie, M., Johnson, J., Boyle, T. A., Ruffell, B., Perez, B. A., Antonia, S. J., et al. (2023) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-22-0927 · Cited by 17

Dissecting the single-cell transcriptome network of macrophage and identifies a signature to predict prognosis in lung adenocarcinoma

Hu, Z., Jin, X., Hong, W., Sui, Q., Zhao, M., Huang, Y., Li, M., Wang, Q., Zhan, C., & Chen, Z. (2023) · Cellular Oncology · doi:10.1007/s13402-023-00816-7 · Cited by 18

Tumor heterogeneity and immune-evasive T follicular cell lymphoma phenotypes at single-cell resolution

Suma, S., Suehara, Y., Fujisawa, M., Abe, Y., Hattori, K., Makishima, K., Sakamoto, T., Sawa, A., Bando, H., Kaji, D., et al. (2023) · Leukemia · doi:10.1038/s41375-023-02093-7 · Cited by 17

Pan‐Cancer Single‐Nucleus Total RNA Sequencing Using snHH‐Seq

Chen, H., Fang, X., Shao, J., Zhang, Q., Xu, L., Chen, J., Mei, Y., Jiang, M., Wang, Y., Li, Z., et al. (2023) · Advanced Science · doi:10.1002/advs.202304755 · Cited by 17

Clusterin protects mature dendritic cells from reactive oxygen species mediated cell death

Malizia, Á. L., Merlotti, A., Bonté, P., Sager, M., Arribas, Y. A., Goudot, C., Díaz, F. A. E., Pereyra-Gerber, P., Ceballos, A., Amigorena, S., et al. (2023) · OncoImmunology · doi:10.1080/2162402x.2023.2294564 · Cited by 17

Single-cell transcriptome analysis reveals immunosuppressive landscape in overweight and obese colorectal cancer

Xiao, G., Zheng, Y., Chen, H., Luo, M., Yang, C., Ren, D., Qin, P., Zhang, H., & Lin, H. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-04921-5 · Cited by 17

Network-based screening identifies sitagliptin as an antitumor drug targeting dendritic cells

Ng, I.-I., Zhang, J., Tian, T., Qi, P., Huang, Z., Xiao, K., Yao, X., Ng, L., Zeng, J., & Tang, H. (2024) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2023-008254 · Cited by 17

Single-cell landscape of undifferentiated pleomorphic sarcoma

Lu, Y., Chen, D., Wang, B., Chai, W.-J., Yan, M., Chen, Y., Zhan, Y., Yang, R., Zhou, E., Dai, S., et al. (2024) · Oncogene · doi:10.1038/s41388-024-03001-8 · Cited by 17

Role of Tumor-Associated Macrophages in Cervical Cancer: Integrating Classical Perspectives with Recent Technological Advances

Choi, Y., Lee, D. H., Kim, N. Y., Seo, I., Park, J. Y., & Chong, G. O. (2024) · Life · doi:10.3390/life14040443 · Cited by 19

Single-cell transcriptome reveals highly complement activated microglia cells in association with pediatric tuberculous meningitis

Mo, S., Shi, C., Cai, Y., Xu, M., Xu, H., Xu, Y., Zhang, K., Zhang, Y., Liu, J., Che, S., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1387808 · Cited by 18

Revealing the crucial roles of suppressive immune microenvironment in cardiac myxoma progression

Jiang, Z., Kang, Q., Qian, H., Xu, Z., Tong, H., Yang, J., Li, L., Li, R., Li, G., Chen, F., et al. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01912-2 · Cited by 17

The role of long non‐coding RNA Maternally Expressed Gene 3 in cancer‐associated fibroblasts at single cell pan‐cancer level

Zhou, T., Yan, H., Deng, Y., Zhu, Y., Xia, X., Wu, W., Zhang, W., Chen, H., Hu, J., Zhou, Z., et al. (2024) · Interdisciplinary medicine · doi:10.1002/inmd.20240018 · Cited by 17

Dissection of intratumor microbiome–host interactions at the single-cell level in lung cancer

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